[BioC] limma makeContrasts

[Gerhard Thallinger]

Dear Ben,

> ....
> This means I have on Slide 1: 18j (Cy3) vs 25n (Cy5), Slide 
> 2: 18n (Cy3) 
> vs 29j (Cy5), etc. This is an unconnected design. So I tried to use 
> Chapter 9 (Separate Channel Analysis of Two-color Data) of the limma 
> User's manual. When I try to make a contrast, I am getting an error:
> 
>  > Cont.18<-makeContrasts(18j-18n,levels=design)
> Error: syntax error in "Cont.18<-makeContrasts(18j"
> 
> When I try to use "", I am getting also an error:
> 
>  > Cont.18<-makeContrasts("18j-18n",levels=design)
> Error in parse(file, n, text, prompt) : syntax error in "18j"
> 
> Does anybody knows where the error occurs? What am I doing wrong?

  Nothing wrong on your side. This is a "feature" of makeContrasts(), 
  constrasts must not start with a digit. Put a letter in 
  front of your Target definition. Everything should work fine then.

Regards

Gerhard